When you customize ltsp by symlinking /opt/ltsp to another dir (i.e. ln -s /srv/ltsp /opt/ltsp), the command ltsp-update-sshkeys doesn't find arch root directories.
As administrator would potentially change ltsp root directory by using symbolic links, I think that a good practice would be to terminate all searched directories in find command by a "/" to be sure it will follows symlinks (the patch below).
diff /usr/sbin/ltsp-update-sshkeys ltsp-update-sshkeys
< clients=$(find /opt/ltsp -mindepth 1 -maxdepth 1 -type d -printf '%f\n')
> clients=$(find /opt/ltsp/ -mindepth 1 -maxdepth 1 -type d -printf '%f\n')
I fixed this bug, by adding a '/' to the end of the directory that is being searched in the "find" command. The new version is now available on the LTSP download page.